Hidden Markov Model for Solar Geolocation Archival Tags

Estimate positions of animal from data collected by solar geolocation archival tags.


Welcome to FLightR, an R package that deals with solar geolocation data. The scope of the package is to position animal using data from solar geolocation archival tags the package is in the active development.

to install the package try:


--------------- Version 0.4.4 All function names started from plot. are replaced wit plot_, e.g. plot.lon.lat() became plot_lon_lat() Version 0.3.9 has got two major changes:

  1. Workflow was completely rewtitten and simplified. Updated workflow is here
  2. New version does not require lots of RAM, but it became slower.

Very important changes were made for version 0.3.6 Just contact me if results come out strange.

##Examples of packages use:

  1. new (>=0.3.9) workflow for black-tailed godwit example with Intigeo tag
  2. old (<0.3.9) workflow for tree swallow example with BAS tag
  3. old (<0.3.9) workflow for black-tailed godwit example with Intigeo tag

Do not know what the difference between BAS and Intigeo is? In short intigeo are being currently produced by Migrate Technology Ltd, and measure data up to very high sun elevation angles, BAS tags are the old ones produced inititally by British Antarctic Survey, then by Migrate Technology (till ~2013) and Lotek (still available) and measured data at the low sun angles (with maximum written at 64). More on the tag specific differences can be found here.

Vignette for the package is coming very soon,

I am also developing [wiki pages for the package] (https://github.com/eldarrak/FLightR/wiki)


  1. Rakhimberdiev, E., Winkler, D.W., Bridge, E., Seavy, N.E., Sheldon, D., Piersma, T. & Saveliev, A. (2015). A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity. Movement Ecology, 3, 25. Check it

  2. Rakhimberdiev, E., Senner, N.R., Verhoeven, M.A., Winkler, D.W., Bouten, W. & Piersma, T. (2016). Comparing inferences of solar geolocation data against high-precision GPS data: annual movements of a double-tagged black-tailed godwit. Journal of Avian Biology, 47, 589–596. Check it

  3. Rakhimberdiev, E. (2016). Ornithology by light levels today: dealing with a developing teenager. Wader Study, 123, 1–3.

  4. Rakhimberdiev, E.Saveliev A., Piersma, T. & Karagicheva, J. FLightR: An R package for reconstructing animal paths from solar geolocation loggers - submitted

Discussion web forum for solar geolocation is available at ornithologyexchange. Ask there if you need help with the FLightR per se or with solar geolocation in general.


Reference manual

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0.4.6 by Eldar Rakhimberdiev, 6 months ago


Report a bug at http://github.com/eldarrak/FLightR/issues

Browse source code at https://github.com/cran/FLightR

Authors: Eldar Rakhimberdiev <eldar@nioz.nl> with contributions from Anatoly Saveliev and Julia Karagicheva

Documentation:   PDF Manual  

GPL-3 license

Imports bit, ggsn, ggmap, ggplot2, CircStats, circular, GeoLight, fields, maptools, methods, mgcv, nlme, parallel, raster, RcppArmadillo, rgdal, rgeos, sp, truncnorm

Suggests covr, testthat, knitr, rmarkdown

See at CRAN